To clear into Panama by private yacht, sail to a port of entry, fly the yellow Q flag, and stay aboard until you have seen the officials. The skipper takes the ship's papers, crew list, passports and the zarpe from your last port to Migración (immigration) and to the Autoridad Marítima de Panamá (AMP) port captain, who issues the cruising permit. Depending on the port, Aduanas (customs) and a health officer also inspect. The order and the fees vary by port, so confirm locally.
The short version
Clearing in to Panama is a paper process run by several agencies, and you see each one in turn. In practice it looks like this:
- Arrive at a port of entry and call the port or marina on VHF. On the Caribbean side, Cristóbal Signal Station answers on VHF 12 or 16 and directs yachts to the anchorage or to Shelter Bay Marina.
- Fly the Q flag and keep everyone aboard until you are cleared. Only the skipper goes ashore to the offices unless an official asks for the crew.
- Migración stamps passports and records the crew.
- The AMP port captain (Capitanía de Puerto) clears the vessel in and processes the cruising permit (permiso de navegación).
- Aduanas and a health officer inspect where they are posted; at some ports they board the boat.
- Lower the Q flag, raise the Panamanian courtesy flag, and keep copies of everything aboard for boardings by SENAN.
A 2025 executive decree on nautical tourism (Decreto Ejecutivo 4 of 2025) tells Migración, Aduanas and the AMP to work from a single window (Ventanilla Única) at marinas, coordinated by the AMP, and to accept digital documents from visiting yachts. How far that has reached each port is uneven, so plan for the traditional office-by-office routine and enjoy it if it is faster.
Who you see, and what each office does
| Office | What it does for a yacht | Notes |
|---|---|---|
| Servicio Nacional de Migración | Entry stamps for skipper and crew; records the crew list | At Shelter Bay, cruisers report Migración is seen first, then the port captain |
| AMP Capitanía de Puerto | Clears the vessel in, issues the cruising permit and later the zarpe | Not every arrival point has one; Porvenir currently does not, per noonsite (March 2025) |
| Autoridad Nacional de Aduanas | Customs declaration and the boat's temporary admission | Posted at main ports; at Bocas del Toro cruisers report a customs charge |
| Health / quarantine (Ministerio de Salud, MINSA) | Health clearance of the vessel | Present at some ports, such as Bocas and the Chiriquí side; often absent elsewhere |
| SENAN | Maritime enforcement, boardings at sea | Not a clearance office as such, but in some remote places such as Puerto Obaldía a police checkpoint records you first |
For office addresses in the capital, see marine offices and contacts in Panama City.
Documents to have ready
- Ship's papers: original registration or documentation certificate, plus copies.
- Crew list: printed, signed by the captain, several copies. Forms are available at the port captain's office at Shelter Bay.
- Passports for everyone aboard, plus copies. Passports should generally have at least three months' validity left.
- The zarpe from your last port, the international clearance you received when leaving the previous country. Without it, expect questions.
- Previous Panamanian paperwork if you are already cleared in and arriving at a new port: cruising permit copy and domestic zarpe.
- Pet papers if you carry animals, and a list of firearms if any are aboard; both need advance arrangements.
Cruisers consistently report needing three or four copies of each document. There is a print shop at Shelter Bay; elsewhere print before you arrive.
Cruising permit, pre-arrival notice and fees
If you are only transiting the Canal, noonsite reports you do not need a cruising permit. If you stay and cruise, the AMP issues one; at Shelter Bay noonsite says it is needed for stays over 14 days and the marina handles the application with the port authority in Colón. The 2025 decree grants foreign yachts a free special navigation permit for the first three months and keeps them exempt from arrival and anchoring fees for stays of up to a year. Ask the port captain how that applies to you on the day. Full detail: the Panama cruising permit.
Pre-arrival notification. We found no general online pre-arrival system for private yachts on an official site. The decree says authorities must accept digital documents, and some port captains ask you to email your paperwork ahead. Send it if you can; it rarely hurts.
Fees. No current official tariff is published for yacht clearance. Cruiser reports on noonsite give a picture, not a price list: clearing in at Shelter Bay on a weekday reported free (February 2025) with a US$75 weekend surcharge; Bocas del Toro reported health US$20 and customs US$40 (December 2022). Most charges are paid in cash at the office that levies them. Confirm the current figures with the AMP (+507 501-5000) before you budget.
Pacific vs Caribbean arrivals
Caribbean side
Most yachts from Florida, the Bahamas and the western Caribbean arrive at Colón. Shelter Bay Marina has Migración and the port captain on site Monday to Friday, which makes it the simplest clear-in in the country. Linton Bay (Puerto Lindo) has a port captain but immigration is in Portobelo. Porvenir in San Blas has Migración and the Guna Congress but, per noonsite, no port captain at present, so you finish the cruising permit later in Puerto Lindo or Colón. Bocas del Toro has all offices in town. If you stop in San Blas, the Guna Yala fees come on top; see San Blas permits and fees.
Pacific side
Arrivals from Costa Rica, the Galápagos or Mexico usually clear in at Balboa near Panama City, or in Chiriquí, where officials come from Pedregal. Panama City's offices are spread out, so allow a full day. Pacific tides of 4 to 6 metres matter at dinghy landings; time your trips ashore. The full list is in Panama ports of entry by sea.
After you are cleared in
Once cleared, you move between Panamanian ports with your cruising permit and, where the port captain asks for it, a domestic zarpe; see zarpe explained. Watch your crew's stay limits (visa rules for boat crew) and the boat's own time limit (temporary import of a foreign yacht). When it is time to go, leaving Panama by boat covers the exit stamps and the international zarpe.
Your practical starting checklist
- Choose a port of entry with the offices you need open, and aim to arrive on a weekday morning.
- Print the crew list and make three or four copies of passports, registration and your last zarpe.
- Call the port or marina on VHF on approach and follow its anchoring or berthing instructions.
- Fly the Q flag and keep crew aboard; the skipper goes to Migración, then the AMP port captain.
- Allow Aduanas and health officers aboard if they inspect, and get a receipt for every payment.
- Apply for the cruising permit if you will stay and cruise, and keep all originals and copies aboard.
Frequently asked questions
Do I need an agent to clear into Panama by yacht?
No. Private yachts can clear in themselves. Agents save time, especially in Panama City and for Canal transits, and the marina office at Shelter Bay helps with the cruising permit application.
Can I clear in at the weekend?
Usually, but expect overtime charges. Noonsite reports a US$75 extra for weekend clearance at Shelter Bay (February 2025), and the Bocas del Toro port captain closes at 3 pm on weekdays.
Is there an online pre-arrival form for yachts?
We could not find a general online pre-arrival system for private yachts on an official site. A 2025 decree requires authorities to accept digital documents; email your papers to the port captain ahead where you can.
¿Qué oficinas visito al llegar a Panamá en velero?
Migración para los sellos de pasaporte, la Capitanía de Puerto de la AMP para la entrada de la embarcación y el permiso de navegación, y Aduanas y Salud donde estén presentes. Confirme horarios y tarifas en el puerto de entrada.
En español: entrar a Panamá en yate
Para entrar a Panamá en yate privado, llegue a un puerto de entrada, ice la bandera Q y permanezca a bordo hasta completar los trámites. El capitán presenta los documentos de la embarcación, la lista de tripulantes, los pasaportes y el zarpe del último puerto ante Migración y la Capitanía de Puerto de la Autoridad Marítima de Panamá (AMP), que tramita el permiso de navegación. Aduanas y Salud inspeccionan en algunos puertos. Confirme horarios y tarifas localmente.
The next question to answer
Every guide on entering and leaving Panama by sea. Read Arrival & clearance in Panama.
Where you can clear in on each coast, and who is there. Read Panama ports of entry by sea.
The permiso de navegación: who needs it, cost, validity. Read Panama cruising permit.
Same topic in Florida: coming from the US? Compare Returning to Florida by Boat: Entry Procedures.
Official resources
Use the relevant Panamanian authority for current requirements and fees. These resources are the next place to check; a practical recommendation is not an agency determination.
- Gaceta Oficial: Decreto Ejecutivo No. 4 de 11 de febrero de 2025, reglamentación del turismo náutico (arts. 2, 3, 12–14, 16) ↗
- Noonsite: Cristóbal/Colón clearance (updated Feb 2025) — secondary, cruiser-reported ↗
- Noonsite: Porvenir (San Blas) clearance (updated Mar 2025) — secondary, cruiser-reported ↗
- Noonsite: Bocas del Toro clearance (updated Dec 2022) — secondary, cruiser-reported ↗
- AMP: nota de prensa, AMP y marinas de Bocas del Toro (contact [email protected], +507 501-5000) ↗
- Superyacht Services Guide: Panama formalities overview — secondary ↗